Alcoholic liver disease and cirrhosis (ALD) is a leading cause of alcohol-related death and disability. Hepatic encephalopathy (HE) is a serious complication of ALD and is characterized by a spectrum of neuro-cognitive dysfunction. The pathogenesis of HE is driven by intestinal microflora-derived factors, the host response to these factors, the impact of these factors on hepatic function, the severity of the underlying liver disease and portasystemic shunting. In ALD, another layer of complexity is added by the direct effects of alcohol on cognitive function and its indirect effects on the other factors that drive HE. Thus, the gut-liver-brain axis represents a complex system and its perturbation in ALD plays a central role in the genesis of HE in ALD. Unfortunately, in both HE and ALD, most of the literature has focused on end-organs rather than consider them a complex biologic system. The impact of the interactions between the intestinal microflora, intestine, liver and the brain in the genesis of HE in ALD has therefore not been fully explored. This gap in our knowledge has hindered the investigation of the mechanisms of alcohol-induced gut, liver and brain injury in the context of HE. In this proposal, we will address this unmet need by testing the central hypothesis that: patients with alcoholic cirrhosis have a specific alteration in their gut flora population and function that is linked with a pro- inflammatory milieu and endotoxemia and associated impaired brain function and hepatic encephalopathy, compared to those who do not have alcoholic cirrhosis.. We will test this hypothesis by the following specific aim: To determine the association between changes in gut microflora function and population and their associated effects on cognition in patients with alcoholic cirrhosis and hepatic encephalopathy compared to those with non-alcoholic cirrhosis using a systems biology approach. Subjects with ALD and cirrhosis (with or without HE) will be compared to those with cirrhosis (with or without HE) due to non- alcoholic fatty liver disease (NAFLD). The phenome, the microbiome, the metabolome and the meta- transcriptome will be studied in each patient. The phenome will be characterized by alcohol use, cirrhosis severity, presence of HE, cognitive function (psychometric tests, brain MR spectroscopy (MRS) and diffusion tensor imaging) and systemic inflammatory state (endotoxin and endothelial dysfunction). The gut microbiome will be analyzed using Length-heterogeneity PCR and Multi-tagged pyrosequencing (MTPS) of stool and colonic mucosa. The metabolome will be studied using urine and serum MRS, and the meta-transcriptome or functional capacity of the gut microflora will be assayed using deep MTPS. The final Systems Biology analysis will demonstrate key linkages between HE and ALD that will delineate specific targets that could form the focus of future trials. It will also define distinctions in the HE pathogenesis in ALD compared to NAFLD that would shed light into the mechanistic differences of HE development in these divergent diseases. The investigators are well suited to perform these studies because of their expertise, availability of subjects and the environment. PUBLIC HEALTH RELEVANCE: Patients who drink alcohol can hurt their liver, brain as well as change the bacteria in their bowels, all of which can affect their quality of life and survival long after they quit drinking. This proposal will study whether change in the bowel bacteria can explain these effects of alcohol on the brain as well as the entire body by comparing patients who used to drink to those who do not drink. The results will help us find newer targets for treatments to prevent these injurious effects of alcohol on the bowels, liver and brain